2019 Genomics of Disease in Wildlife Workshop
Course Content and Tentative Schedule
Schedule will be continuously updated so check back often!
We will post as much material as possible as soon as possible. Our intent is to leave this material online indefinitely.
Sunday June 2, 2019. Pre-workshop clinic and Opening Reception
Room 304-306 and Longs Peak Room, Lory Center
Pre-workshop command line clinic (10:00 - 16:00)
| Time | Activity |
|---|---|
| 10:00-10:15 | Opening Remarks - Introduction to the Lab Computers |
| 10:15-11:45 | Bob Fitak - The UNIX Command line Lecture and Tutorial |
| 11:45-12:15 | Mark Stenglein - Principles of Computing Lecture |
| 12:15-13:15 | Lunch provided onsite |
| 13:15-14:30 | Mark Stenglein - Command Line Part 2 |
| 14:30-14:45 | Coffee break |
| 14:45-16:00 | Bob Fitak - An Introduction to R and R Studio - Tutorial |
| 18:30-21:30 | Don't Miss the Opening Reception!!!! |
Welcome and opening reception (18:30 - 21:30)
| Time | Activity |
|---|---|
| 18:30-18:40 | Welcome and Opening Remarks, Sue VandeWoude and Jill Pecon Slattery |
| 18:40-18:50 | Instructors and Team Introductions |
| 18:50-19:35 | 10 Attendee Presentations |
| 19:35-20:00 | Introduction to the group exercise, Bob Fitak: Scenarios Powerpoint |
| 20:00-21:30 | Refreshments and Social Time |
Monday June 3, 2019. Day 1: NGS Data Overview, Genome Mining
Lory Center Room 304-306
| Time | Activity |
|---|---|
| 07:00–08:00 | Breakfast, Rams Horn Dining Center |
| 08:15-08:25 | Step 1: What are my NGS tools for wildlife disease research? Jill Pecon Slattery |
| 08:25-08:35 | Introduction to workshop computers, Joe Strecker |
| 08:35-10:00 | Intro to genomics and NGS, Mark Stenglein |
| 10:00-10:20 | Coffee Break |
| 10:20-12:15 | BLAST Lecture and Tutorial, Bob Fitak |
| 12:15-13:15 | Lunch Provided Onsite |
| 13:15-14:15 | 10 Attendee Presentations |
| 14:15-14:45 | Obtaining data, Mark Stenglein |
| 14:45-15:30 | Data Quality Control Lecture and Exercise, Bob Fitak |
| 15:30-16:00 | Group projects time |
| 16:00-17:00 | Tour of CSU Veterinary Teaching Hospital |
| 17:00-19:00 | Free time and dinner, Rams Horn Dining Center |
| 19:30-21:00 | Optional computer time with instructors |
Tuesday June 4, 2019: Genome Mapping, Assembly, and Metagenomics
| Time | Activity |
|---|---|
| 07:00–08:00 | Breakfast, Rams Horn Dining Center |
| 08:15-08:25 | Step 2: Best Practices for Generating Quality Genomes of Host and Pathogen, Jill Pecon Slattery |
| 08:25-09:30 | Mapping to Reference Genomes Lecture, Bob Fitak (Mapping activity Template) |
| 09:30-10:00 | Flash Talk, Karen Fox, CO Parks & Wildlife |
| 10:00-10:20 | Coffee Break and Meet Invited Speaker |
| 10:20-11:15 | Mapping Exercise, Bob Fitak and Mark Stenglein |
| 11:15-12:15 | Genome Assembly Lecture, Mark Stenglein |
| 12:15-13:15 | Lunch Provided Onsite |
| 13:15-15:15 | Genome Assembly Exercise, Mark Stenglein and Bob Fitak |
| 15:15-15:35 | Coffee Break |
| 15:35-16:35 | Genome Assembly exercises continued, and Metagenomics and Disease Lecture, Mark Stenglein and Bob Fitak |
| 16:35-17:00 | Group projects time |
| 17:00-19:00 | Free time and dinner, Rams Horn Dining Center |
| 19:30-20:30 | Plenary Speaker, Loren Cassin-Sackett, University of South Florida |
| 20:30-22:00 | Social Hour with Invited Speaker |
Wedendsday June 5, 2019: Multiple Sequence Alignments and Phylogenomics
| Time | Activity |
|---|---|
| 07:00–08:00 | Breakfast, Rams Horn Dining Center |
| 08:15-08:25 | Step 3: Comparing Differences Within and Between Genomes, Jill Pecon Slattery |
| 08:25-09:00 | Introduction to Multiple Sequence Alignments of Targeted & Whole Genomes, Jill Pecon Slattery |
| 09:00-09:30 | Alignment Computer Lab: Part 1, Jill Pecon Slattery and Justin Lee Instructions |
| 09:30-10:00 | CSU Flash Talk, Sue VandeWoude and Jenn Malmberg |
| 10:00-10:20 | Coffee Break and Meet Invited Speaker |
| 10:20-10:50 | Alignment computer lab: Part 2, Jill Pecon Slattery and Justin Lee exercise files |
| 10:50-11:30 | The basics of phylogenomic trees: Models, Search Algorithms, Tree Scores, Topology Roman Biek |
| 11:30-12:00 | Phylogenomic Inferences of host/pathogen Jill Pecon Slattery |
| 12:15-13:15 | Lunch Provided Onsite |
| 13:15-15:15 | Phylogenomic Reconstruction Lab: jModeltest ML, ME MP, MCRobot demo, Jill Pecon Slattery, Justin Lee, Roman Biek, Bob Fitak exercise files |
| 15:15-15:35 | Coffee Break |
| 15:35-17:00 | Phylogenomic Reconstruction Lab: MrBayes, Justin Lee |
| 17:00-19:30 | Free time and dinner, Rams Horn Dining Center |
| 19:30-20:30 | Plenary Speaker, Roman Biek, University of Glasgow |
| 20:30-21:30 | Social Hour with Invited Speaker |
Thursday June 6, 2019: Tree-based Inferences in Host-Pathogen Ecology and Evolution: Clocks, Transmission and Adaptation
| Time | Activity |
|---|---|
| 07:00–08:00 | Breakfast, Rams Horn Dining Center |
| 08:15-08:25 | Step 5: Genomics of Host-pathogen Interaction |
| 08:35-09:30 | Detecting and quantifying variants: lecture and exercise, Mark Stenglein |
| 09:30-10:00 | CSU Flash Talk, Rebekah Kading and Anna Fragre |
| 10:00-10:20 | Coffee Break and Meet Invited Speaker |
| 10:20-11:15 | Lectures: Intro to concepts of molecular clocks, timescale, patterns of neutral evolution, TMRCA, Roman Biek |
| 11:15-12:15 | Lab BEAST, part 1, Justin Lee |
| 12:15-13:15 | Lunch Provided Onsite |
| 13:15-14:15 | Lab BEAST, part 2, Roman Biek, Justin Lee |
| 14:15-15:05 | Lecture: Phylodynamics of Measurably Evolving Pathogens, Roman Biek |
| 15:05-15:35 | Lecture: Signals of Selection in Host Genome, Jill Pecon Slattery lecture |
| XX:XX-XX:XX | Computer Labs: Selection, Adaptation, Variant Detection: PAML and HyPhy, Jill Pecon Slattery (ran out of time: didn't get to this). exercise files |
| 16:00-18:30 | Hike, weather permitting, Edit Szalai |
| 17:00-19:00 | Free time and dinner, Rams Horn Dining Center |
| 19:00-21:00 | Optional computer time with instructors |
Friday June 7, 2019: Population Genomics
| Time | Activity |
|---|---|
| 07:00–08:00 | Breakfast, Rams Horn Dining Center |
| 08:15-08:25 | Step 4: Applying my genomic tools across populations within host & pathogen, Jill Pecon Slattery |
| 08:25-09:30 | Population Genomics 101, Chris Funk |
| 09:30-10:00 | CSU Flash Talk, Chistie Mayo |
| 10:00-10:20 | Coffee Break and Meet Invited Speaker |
| 10:20-11:00 | Population Genomics 101 (continued), Chris Funk |
| 11:00-11:30 | Host Population Genomics in Disease: Landscape Genomics, Daryl Trumbo |
| 11:40-12:15 | Computer Lab: Population Genomics, Chris Funk and Daryl Trumbo |
| 12:15-13:15 | Lunch Provided Onsite |
| 13:15-15:15 | Computer Lab: Population Genomics, Chris Funk and Daryl Trumbo |
| 15:15-15:35 | Coffee Break |
| 15:35-17:00 | Computer Lab: Population Genomics, Chris Funk and Daryl Trumbo |
| 18:00-??:?? | Party, Old Town Fort Collins. The Blind Pig, 214 Linden Street |
Saturday June 8, 2019: Putting it all together: group project presentations
| Time | Activity |
|---|---|
| 07:00–08:00 | Breakfast, Rams Horn Dining Center |
| 08:15-08:20 | Step 6: Our Workflow & GDW2019 Publication, Jill, Bob, Sue, Chris, Mark |
| 08:20-09:00 | Group 1 Project Presentation |
| 09:00-09:40 | Group 2 Project Presentation |
| 09:40-10:00 | Coffee Break |
| 10:00-10:40 | Group 3 Project Presentation |
| 10:40-11:20 | Group 4 Project Presentation |
| 11:20-11:40 | Concluding Remarks & Farewells, instructors & participants |
Other materials